Variant report

Variant	rs2299999
Chromosome Location	chr7:107877066-107877067
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107872529..107874064-chr7:107876673..107878987,2	K562	blood:
2	chr7:107872262..107874064-chr7:107876673..107879792,3	K562	blood:
3	chr7:107876262..107880228-chr7:107881890..107885799,6	MCF-7	breast:
4	chr7:107867953..107871248-chr7:107875494..107877512,3	K562	blood:
5	chr7:107876529..107879004-chr7:107987282..107988913,2	MCF-7	breast:
6	chr7:107875919..107879623-chr7:107880084..107882583,5	K562	blood:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10487842	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10487843	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10953560	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11978605	0.91[ASN][1000 genomes]
rs11980184	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11980771	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11984362	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12531607	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12534073	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12534706	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12536606	0.94[EUR][1000 genomes]
rs12538125	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1269639	0.92[JPT][hapmap]
rs12705439	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13228054	0.80[EUR][1000 genomes]
rs13228675	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13231463	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13237289	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13242621	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13245910	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13247108	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1548950	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17155187	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17155196	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17155335	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs17331230	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2111203	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2191046	0.86[EUR][1000 genomes]
rs2193252	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2193253	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2193254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267876	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2267877	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2272617	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2284284	0.82[EUR][1000 genomes]
rs2299992	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2299996	0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2300000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300002	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34723270	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34754517	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55643449	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67133820	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6958333	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6964282	0.96[EUR][1000 genomes]
rs6977003	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6980041	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71568512	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73199565	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7776972	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7783282	0.85[AMR][1000 genomes]
rs7784186	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789291	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7795834	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7796675	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7809003	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv831089	chr7:107687618-107877240	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107830400-107886400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:107860600-107886600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:107863800-107877200	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:107867800-107878000	Weak transcription	Brain Angular Gyrus	brain
5	chr7:107871200-107880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:107871200-107886400	Weak transcription	Brain Anterior Caudate	brain
7	chr7:107871600-107879800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:107874400-107879200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:107874600-107878000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:107874800-107886200	Weak transcription	HSMMtube	muscle
11	chr7:107875000-107877600	Enhancers	Primary hematopoietic stem cells	blood
12	chr7:107875200-107877600	Enhancers	HUVEC	blood vessel
13	chr7:107875200-107881200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr7:107875600-107877800	Enhancers	Fetal Intestine Small	intestine
15	chr7:107875600-107879600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr7:107875800-107877800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr7:107875800-107881600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr7:107876000-107877800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr7:107876000-107877800	Enhancers	Placenta	Placenta
20	chr7:107876000-107877800	Enhancers	Pancreas	Pancrea
21	chr7:107876000-107878000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:107876000-107878400	Enhancers	Fetal Intestine Large	intestine
23	chr7:107876000-107881000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:107876000-107881200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr7:107876200-107877400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:107876200-107878000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:107876200-107878200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr7:107876200-107878600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr7:107876200-107880800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr7:107876200-107881200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr7:107876200-107881200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:107876200-107881200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr7:107876400-107877600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:107876400-107886400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:107876600-107877600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:107876600-107877600	Weak transcription	GM12878-XiMat	blood
37	chr7:107876600-107877800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:107877000-107877200	Enhancers	A549	lung
39	chr7:107877000-107877400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr7:107877000-107877600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:107877000-107877600	Enhancers	K562	blood
42	chr7:107877000-107885600	Weak transcription	HSMM	muscle
43	chr7:107877000-107886200	Weak transcription	HMEC	breast

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